Basic Usage Guide

1. Basic usage pattern

   linc-convert <MODALITY> <PIPELINE> [ARGS] [OPTIONS]
   

2. The top-level help lists all modalities (data families) and global flags.

   linc-convert --help
   

3. Each modality contains one or more pipelines (subcommands).

   linc-convert psoct --help
   

4. Show the detailed help for a pipeline, including the input, output, chunking, sharding and additional flags.

   linc-convert psoct single_volume --help
   

5. Basic conversion example

   linc-convert psoct single_volume IN.mat -o OUT.zarr
   

6. Convert to NIfTI-Zarr and provide the custom key for the MATLAB array

   linc-convert psoct single_volume IN.mat --key Psi_ObsLSQ -o OUT.nii.zarr
   

7. Convert to Zarr version 3 with sharding

   linc-convert psoct single_volume IN.mat -o OUT.zarr --zarr-version 3 --shard 1024